> Date: Tue, 19 Feb 2013 17:50:05 -0500
> From: fischl@nmr.mgh.harvard.edu
> To: horton_paul@hotmail.com
> Subject: RE: [Freesurfer] mri_ca_label problem
>
> just to rule out a longshot, can you send me the output of printenv?
>
>
> On Tue, 19 Feb 2013, paul horton wrote:
>
> > Hi Bruce,
> >  
> > When I run recon -all the last thing it prints before going to the
> > command prompt is
> >  
> > 'recon-all exited with ERRORS at Mon Feb 18 19:22:12 GMT 2013'
> >  
> > and when I run the stand alone command, i.e. mri_ca_label, the last thing it
> > prints before going to the command prompt is
> >  
> > 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt'
> >  
> > I hope this information helps.
> >  
> > Thanks
> >  
> > Paul
> >  
> >  
> >  
> > > Date: Tue, 19 Feb 2013 17:28:52 -0500
> > > From: fischl@nmr.mgh.harvard.edu
> > > To: horton_paul@hotmail.com
> > > CC: freesurfer@nmr.mgh.harvard.edu
> > > Subject: RE: [Freesurfer] mri_ca_label problem
> > >
> > > and that's the last thing it prints before returning to a prompt?
> > > On Tue, 19
> > > Feb 2013, paul horton wrote:
> > >
> > > > Hi Bruce,
> > > >  
> > > > Yes this is within recon-all. I have also tried it as a stand alone
> > command
> > > > but it stops at the same place, i.e. when the function outputs the
> > following
> > > > statement: 'saving intensity scales to
> > > > aseg.auto_noCCseg.label_intensities.txt'. The file
> > 'aseg.auto_noCCseg.mgz'
> > > > is not saved but the file 'aseg.auto_noCCseg.label_intensities.txt' is. 
> > > > Yes, it is writeable and there is enough disk space.  The only error
> > > > messages I get refer to the functions not finding the relevant files as
> > > > they were not saved.  I have attached the log below:
> > > >  
> > > > #--------------------------------------
> > > >
> > > > #@# SubCort Seg Mon Feb 18 19:02:14 GMT 2013
> > > >
> > > > mri_ca_label -align -nobigventricles norm.mgztransforms/talairach.m3z/software/system/freesurfer/freesurfer-4.5.0//avera
> > ge/RB_all_2008-03-26.gca
> > > > aseg.auto_noCCseg.mgz
> > > >
> > > > renormalizing sequences with structure alignment, equivalent to:
> > > >
> > > > -renormalize
> > > >
> > > > -renormalize_mean 0.500
> > > >
> > > > -regularize 0.500
> > > >
> > > > not handling expanded ventricles...
> > > >
> > > > reading 1 input volumes...
> > > >
> > > > reading classifier arrayfrom/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26
> > .gca
> > > > ...
> > > >
> > > > reading input volume from norm.mgz...
> > > >
> > > > average std[0] = 6.9
> > > >
> > > > reading transform from transforms/talairach.m3z...
> > > >
> > > > zcat transforms/talairach.m3z
> > > >
> > > > Atlas used for the 3D morphwas/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-03-26.
> > gca
> > > >
> > > >
> > > > average std = 6.9 using min determinant for regularization = 4.7
> > > >
> > > > 0 singular and 0 ill-conditioned covariance matrices regularized
> > > >
> > > > labeling volume...
> > > >
> > > > renormalizing by structure alignment....
> > > >
> > > > renormalizing input #0
> > > >
> > > > gca peak = 0.15151 (27)
> > > >
> > > > mri peak = 0.15062 (23)
> > > >
> > > > Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels,
> > > > overlap=0.484)
> > > >
> > > > Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels, peak
> > =
> > > > 22), gca=22.3
> > > >
> > > > gca peak = 0.14982 (20)
> > > >
> > > > mri peak = 0.16025 (24)
> > > >
> > > > Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels,
> > > > overlap=0.766)
> > > >
> > > > Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984 voxels,
> > peak =
> > > > 20), gca=20.5
> > > >
> > > > gca peak = 0.28003 (97)
> > > >
> > > > mri peak = 0.11295 (106)
> > > >
> > > > Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels,
> > overlap=0.353)
> > > >
> > > > Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, peak = 104),
> > > > gca=104.3
> > > >
> > > > gca peak = 0.18160 (96)
> > > >
> > > > mri peak = 0.12433 (104)
> > > >
> > > > Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels,
> > overlap=0.638)
> > > >
> > > > Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, peak = 101),
> > > > gca=100.8
> > > >
> > > > gca peak = 0.27536 (62)
> > > >
> > > > mri peak = 0.08252 (69)
> > > >
> > > > Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels,
> > > > overlap=0.818)
> > > >
> > > > Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, peak =
> > 68),
> > > > gca=68.2
> > > >
> > > > gca peak = 0.32745 (63)
> > > >
> > > > mri peak = 0.07934 (66)
> > > >
> > > > Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels,
> > > > overlap=1.000)
> > > >
> > > > Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, peak =
> > 65),
> > > > gca=64.6
> > > >
> > > > gca peak = 0.08597 (105)
> > > >
> > > > mri peak = 0.06861 (109)
> > > >
> > > > Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979
> > voxels,
> > > > overlap=0.744)
> > > >
> > > > Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979
> > voxels,
> > > > peak = 108), gca=107.6
> > > >
> > > > gca peak = 0.09209 (106)
> > > >
> > > > mri peak = 0.07113 (103)
> > > >
> > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels,
> > > > overlap=0.820)
> > > >
> > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels,
> > > > peak = 106), gca=106.0
> > > >
> > > > gca peak = 0.07826 (63)
> > > >
> > > > mri peak = 0.02785 (72)
> > > >
> > > > Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels,
> > > > overlap=0.547)
> > > >
> > > > Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels, peak
> > =
> > > > 71), gca=70.9
> > > >
> > > > gca peak = 0.08598 (64)
> > > >
> > > > mri peak = 0.02894 (68)
> > > >
> > > > Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels,
> > > > overlap=0.642)
> > > >
> > > > Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels,
> > peak =
> > > > 69), gca=68.8
> > > >
> > > > gca peak = 0.24164 (71)
> > > >
> > > > mri peak = 0.13663 (85)
> > > >
> > > > Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels,
> > overlap=0.000)
> > > >
> > > > Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, peak = 82),
> > > > gca=81.7
> > > >
> > > > gca peak = 0.18227 (75)
> > > >
> > > > mri peak = 0.14739 (80)
> > > >
> > > > Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels,
> > overlap=0.988)
> > > >
> > > > Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, peak = 77),
> > > > gca=76.9
> > > >
> > > > gca peak = 0.10629 (62)
> > > >
> > > > mri peak = 0.05203 (64)
> > > >
> > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
> > > > overlap=0.948)
> > > >
> > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
> > peak =
> > > > 64), gca=63.5
> > > >
> > > > gca peak = 0.11668 (59)
> > > >
> > > > mri peak = 0.05041 (65)
> > > >
> > > > Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels,
> > > > overlap=0.926)
> > > >
> > > > Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689 voxels,
> > peak
> > > > = 63), gca=63.4
> > > >
> > > > gca peak = 0.17849 (88)
> > > >
> > > > mri peak = 0.09573 (95)
> > > >
> > > > Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309
> > voxels,
> > > > overlap=0.601)
> > > >
> > > > Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309
> > voxels,
> > > > peak = 95), gca=94.6
> > > >
> > > > gca peak = 0.16819 (86)
> > > >
> > > > mri peak = 0.10076 (95)
> > > >
> > > > Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881
> > voxels,
> > > > overlap=0.590)
> > > >
> > > > Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881
> > voxels,
> > > > peak = 92), gca=92.5
> > > >
> > > > gca peak = 0.41688 (64)
> > > >
> > > > mri peak = 0.07820 (67)
> > > >
> > > > Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels,
> > overlap=1.000)
> > > >
> > > > Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, peak = 66),
> > > > gca=65.6
> > > >
> > > > gca peak = 0.42394 (62)
> > > >
> > > > mri peak = 0.10919 (71)
> > > >
> > > > Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels,
> > overlap=0.434)
> > > >
> > > > Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, peak = 70),
> > > > gca=69.8
> > > >
> > > > gca peak = 0.10041 (96)
> > > >
> > > > mri peak = 0.07146 (97)
> > > >
> > > > Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels,
> > > > overlap=0.910)
> > > >
> > > > Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels, peak
> > =
> > > > 98), gca=98.4
> > > >
> > > > gca peak = 0.13978 (88)
> > > >
> > > > mri peak = 0.06159 (103)
> > > >
> > > > Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels,
> > > > overlap=0.376)
> > > >
> > > > Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels, peak
> > =
> > > > 99), gca=99.0
> > > >
> > > > gca peak = 0.08514 (81)
> > > >
> > > > mri peak = 0.06222 (85)
> > > >
> > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels,
> > overlap=0.964)
> > > >
> > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81),
> > > > gca=81.0
> > > >
> > > > gca peak = 0.09624 (82)
> > > >
> > > > mri peak = 0.09383 (84)
> > > >
> > > > Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels,
> > overlap=0.815)
> > > >
> > > > Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, peak = 84),
> > > > gca=84.0
> > > >
> > > > gca peak = 0.07543 (88)
> > > >
> > > > mri peak = 0.05306 (86)
> > > >
> > > > Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, overlap=0.765)
> > > >
> > > > Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, peak = 92),
> > > > gca=92.4
> > > >
> > > > gca peak = 0.12757 (95)
> > > >
> > > > mri peak = 0.05862 (107)
> > > >
> > > > Right_VentralDC: unreasonable value (111.6/107.0), not in range [80,
> > 110] -
> > > > rejecting
> > > >
> > > > gca peak = 0.17004 (92)
> > > >
> > > > mri peak = 0.06574 (111)
> > > >
> > > > Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110]
> > -
> > > > rejecting
> > > >
> > > > gca peak = 0.21361 (36)
> > > >
> > > > mri peak = 0.12619 (24)
> > > >
> > > > Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels,
> > overlap=0.000)
> > > >
> > > > Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, peak = 25),
> > > > gca=25.2
> > > >
> > > > gca peak = 0.26069 (23)
> > > >
> > > > mri peak = 0.16285 (24)
> > > >
> > > > Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels,
> > overlap=0.640)
> > > >
> > > > Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, peak =
> > 21),
> > > > gca=20.7
> > > >
> > > > gca peak Unknown = 0.94427 ( 0)
> > > >
> > > > gca peak Left_Inf_Lat_Vent = 0.31795 (35)
> > > >
> > > > gca peak CSF = 0.14367 (38)
> > > >
> > > > gca peak Left_Accumbens_area = 0.57033 (70)
> > > >
> > > > gca peak Left_VentralDC = 0.17004 (92)
> > > >
> > > > gca peak Left_undetermined = 1.00000 (35)
> > > >
> > > > gca peak Left_vessel = 0.65201 (62)
> > > >
> > > > gca peak Left_choroid_plexus = 0.09084 (48)
> > > >
> > > > gca peak Right_Inf_Lat_Vent = 0.31129 (32)
> > > >
> > > > gca peak Right_Accumbens_area = 0.30219 (72)
> > > >
> > > > gca peak Right_VentralDC = 0.12757 (95)
> > > >
> > > > gca peak Right_vessel = 0.83418 (60)
> > > >
> > > > gca peak Right_choroid_plexus = 0.10189 (48)
> > > >
> > > > gca peak Fifth_Ventricle = 0.72939 (42)
> > > >
> > > > gca peak WM_hypointensities = 0.14821 (82)
> > > >
> > > > gca peak non_WM_hypointensities = 0.10354 (53)
> > > >
> > > > gca peak Optic_Chiasm = 0.34849 (76)
> > > >
> > > > not using caudate to estimate GM means
> > > >
> > > > estimating mean gm scale to be 1.08 x + 0.0
> > > >
> > > > estimating mean wm scale to be 1.01 x + 0.0
> > > >
> > > > estimating mean csf scale to be 0.86 x + 0.0
> > > >
> > > > Left_Pallidum too bright - rescaling by 1.007 (from 1.050) to 101.5 (was
> > > > 100.8)
> > > >
> > > > Right_Pallidum too bright - rescaling by 0.973 (from 1.075) to 101.5
> > (was
> > > > 104.3)
> > > >
> > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
> > > >
> > > > renormalizing by structure alignment....
> > > >
> > > > renormalizing input #0
> > > >
> > > > gca peak = 0.14515 (23)
> > > >
> > > > mri peak = 0.15062 (23)
> > > >
> > > > Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels,
> > > > overlap=0.897)
> > > >
> > > > Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels, peak
> > =
> > > > 24), gca=23.6
> > > >
> > > > gca peak = 0.19392 (21)
> > > >
> > > > mri peak = 0.16025 (24)
> > > >
> > > > Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels,
> > > > overlap=0.745)
> > > >
> > > > Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984 voxels,
> > peak =
> > > > 21), gca=21.0
> > > >
> > > > gca peak = 0.25607 (102)
> > > >
> > > > mri peak = 0.11295 (106)
> > > >
> > > > Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels,
> > overlap=1.000)
> > > >
> > > > Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, peak = 105),
> > > > gca=104.5
> > > >
> > > > gca peak = 0.17462 (103)
> > > >
> > > > mri peak = 0.12433 (104)
> > > >
> > > > Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels,
> > overlap=0.999)
> > > >
> > > > Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, peak = 103),
> > > > gca=103.0
> > > >
> > > > gca peak = 0.24759 (68)
> > > >
> > > > mri peak = 0.08252 (69)
> > > >
> > > > Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels,
> > > > overlap=0.999)
> > > >
> > > > Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, peak =
> > 68),
> > > > gca=68.0
> > > >
> > > > gca peak = 0.28061 (65)
> > > >
> > > > mri peak = 0.07934 (66)
> > > >
> > > > Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels,
> > > > overlap=0.999)
> > > >
> > > > Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, peak =
> > 62),
> > > > gca=61.8
> > > >
> > > > gca peak = 0.08360 (108)
> > > >
> > > > mri peak = 0.06861 (109)
> > > >
> > > > Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979
> > voxels,
> > > > overlap=0.831)
> > > >
> > > > Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979
> > voxels,
> > > > peak = 108), gca=108.0
> > > >
> > > > gca peak = 0.09206 (106)
> > > >
> > > > mri peak = 0.07113 (103)
> > > >
> > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels,
> > > > overlap=0.820)
> > > >
> > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231 voxels,
> > > > peak = 106), gca=106.0
> > > >
> > > > gca peak = 0.06916 (71)
> > > >
> > > > mri peak = 0.02785 (72)
> > > >
> > > > Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels,
> > > > overlap=0.733)
> > > >
> > > > Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels, peak
> > =
> > > > 69), gca=69.2
> > > >
> > > > gca peak = 0.08227 (69)
> > > >
> > > > mri peak = 0.02894 (68)
> > > >
> > > > Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels,
> > > > overlap=0.734)
> > > >
> > > > Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels,
> > peak =
> > > > 69), gca=69.0
> > > >
> > > > gca peak = 0.22329 (81)
> > > >
> > > > mri peak = 0.13663 (85)
> > > >
> > > > Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels,
> > overlap=1.000)
> > > >
> > > > Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, peak = 81),
> > > > gca=81.0
> > > >
> > > > gca peak = 0.18180 (77)
> > > >
> > > > mri peak = 0.14739 (80)
> > > >
> > > > Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels,
> > overlap=0.937)
> > > >
> > > > Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, peak = 77),
> > > > gca=77.0
> > > >
> > > > gca peak = 0.10419 (63)
> > > >
> > > > mri peak = 0.05203 (64)
> > > >
> > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
> > > > overlap=0.982)
> > > >
> > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
> > peak =
> > > > 65), gca=64.6
> > > >
> > > > gca peak = 0.12084 (64)
> > > >
> > > > mri peak = 0.05041 (65)
> > > >
> > > > Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels,
> > > > overlap=0.985)
> > > >
> > > > Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689 voxels,
> > peak
> > > > = 62), gca=62.4
> > > >
> > > > gca peak = 0.17137 (94)
> > > >
> > > > mri peak = 0.09573 (95)
> > > >
> > > > Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309
> > voxels,
> > > > overlap=0.978)
> > > >
> > > > Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309
> > voxels,
> > > > peak = 94), gca=94.0
> > > >
> > > > gca peak = 0.15715 (93)
> > > >
> > > > mri peak = 0.10076 (95)
> > > >
> > > > Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881
> > voxels,
> > > > overlap=0.983)
> > > >
> > > > Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881
> > voxels,
> > > > peak = 93), gca=93.0
> > > >
> > > > gca peak = 0.32238 (65)
> > > >
> > > > mri peak = 0.07820 (67)
> > > >
> > > > Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels,
> > overlap=1.000)
> > > >
> > > > Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, peak = 65),
> > > > gca=65.0
> > > >
> > > > gca peak = 0.49832 (70)
> > > >
> > > > mri peak = 0.10919 (71)
> > > >
> > > > Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels,
> > overlap=1.000)
> > > >
> > > > Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, peak = 70),
> > > > gca=70.0
> > > >
> > > > gca peak = 0.10606 (98)
> > > >
> > > > mri peak = 0.07146 (97)
> > > >
> > > > Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels,
> > > > overlap=0.901)
> > > >
> > > > Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels, peak
> > =
> > > > 98), gca=98.0
> > > >
> > > > gca peak = 0.12505 (99)
> > > >
> > > > mri peak = 0.06159 (103)
> > > >
> > > > Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels,
> > > > overlap=0.961)
> > > >
> > > > Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels, peak
> > =
> > > > 99), gca=99.0
> > > >
> > > > gca peak = 0.08514 (81)
> > > >
> > > > mri peak = 0.06222 (85)
> > > >
> > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels,
> > overlap=0.964)
> > > >
> > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak = 81),
> > > > gca=81.0
> > > >
> > > > gca peak = 0.09838 (78)
> > > >
> > > > mri peak = 0.09383 (84)
> > > >
> > > > Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels,
> > overlap=0.982)
> > > >
> > > > Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, peak = 78),
> > > > gca=78.0
> > > >
> > > > gca peak = 0.07177 (90)
> > > >
> > > > mri peak = 0.05306 (86)
> > > >
> > > > Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, overlap=0.860)
> > > >
> > > > Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, peak = 92),
> > > > gca=92.2
> > > >
> > > > gca peak = 0.13316 (95)
> > > >
> > > > mri peak = 0.05862 (107)
> > > >
> > > > Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels,
> > overlap=0.010)
> > > >
> > > > Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, peak =
> > 109),
> > > > gca=109.2
> > > >
> > > > gca peak = 0.16834 (92)
> > > >
> > > > mri peak = 0.06574 (111)
> > > >
> > > > Left_VentralDC: unreasonable value (105.8/111.0), not in range [80, 110]
> > -
> > > > rejecting
> > > >
> > > > gca peak = 0.25342 (25)
> > > >
> > > > mri peak = 0.12619 (24)
> > > >
> > > > Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels,
> > overlap=0.998)
> > > >
> > > > Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, peak = 25),
> > > > gca=25.0
> > > >
> > > > gca peak = 0.20850 (21)
> > > >
> > > > mri peak = 0.16285 (24)
> > > >
> > > > Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels,
> > overlap=0.808)
> > > >
> > > > Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, peak =
> > 22),
> > > > gca=21.5
> > > >
> > > > gca peak Unknown = 0.94427 ( 0)
> > > >
> > > > gca peak Left_Inf_Lat_Vent = 0.26363 (36)
> > > >
> > > > gca peak CSF = 0.17919 (33)
> > > >
> > > > gca peak Left_Accumbens_area = 0.40223 (72)
> > > >
> > > > gca peak Left_VentralDC = 0.16834 (92)
> > > >
> > > > gca peak Left_undetermined = 1.00000 (35)
> > > >
> > > > gca peak Left_vessel = 0.63670 (62)
> > > >
> > > > gca peak Left_choroid_plexus = 0.09084 (48)
> > > >
> > > > gca peak Right_Inf_Lat_Vent = 0.29122 (35)
> > > >
> > > > gca peak Right_Accumbens_area = 0.25605 (83)
> > > >
> > > > gca peak Right_vessel = 0.83418 (60)
> > > >
> > > > gca peak Right_choroid_plexus = 0.10189 (48)
> > > >
> > > > gca peak Fifth_Ventricle = 0.81716 (36)
> > > >
> > > > gca peak WM_hypointensities = 0.15216 (83)
> > > >
> > > > gca peak non_WM_hypointensities = 0.09346 (54)
> > > >
> > > > gca peak Optic_Chiasm = 0.34849 (76)
> > > >
> > > > mri_ca_label GCA sequential renormalization: label 28 not consistently
> > > > computed.
> > > >
> > > > not using caudate to estimate GM means
> > > >
> > > > setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0
> > > >
> > > > estimating mean gm scale to be 0.99 x + 0.0
> > > >
> > > > estimating mean wm scale to be 1.00 x + 0.0
> > > >
> > > > estimating mean csf scale to be 1.01 x + 0.0
> > > >
> > > > Left_Pallidum too bright - rescaling by 0.987 (from 1.000) to 101.6 (was
> > > > 103.0)
> > > >
> > > > Right_Pallidum too bright - rescaling by 0.972 (from 1.025) to 101.6
> > (was
> > > > 104.5)
> > > >
> > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
> > > >
> > > > mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz PREDEP40C_fsf
> > > >
> > > > reading input aseg from aseg.auto_noCCseg.mgz
> > > >
> > > > writing aseg with cc labels to aseg.auto.mgz
> > > >
> > > > mri_cc: could not read aseg volumefrom/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.
> > auto
> > > > _noCCseg.mgz
> > > >
> > > > reading asegfrom/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.
> > auto
> > > > _noCCseg.mgz
> > > >
> > > > ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.
> > auto
> > > > _noCCseg.mgz
> > > >
> > > > No such file or directory
> > > >
> > > > #--------------------------------------
> > > >
> > > > #@# Merge ASeg Mon Feb 18 19:22:10 GMT 2013
> > > >
> > > > cp aseg.auto.mgz aseg.mgz
> > > >
> > > > cp: cannot stat `aseg.auto.mgz': No such file or directory
> > > >
> > > > #--------------------------------------------
> > > >
> > > > #@# Intensity Normalization2 Mon Feb 18 19:22:10 GMT 2013
> > > >
> > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri
> > > >
> > > > mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
> > > >
> > > > using segmentation for initial intensity normalization
> > > >
> > > > reading from norm.mgz...
> > > >
> > > > mri_normalize: could not read aseg from file aseg.mgz
> > > >
> > > > using MR volume brainmask.mgz to mask input volume...
> > > >
> > > > ERROR: cannot find
> > > >
> > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/aseg.mgz
> > > >
> > > > No such file or directory
> > > >
> > > > #--------------------------------------------
> > > >
> > > > #@# Mask BFS Mon Feb 18 19:22:11 GMT 2013
> > > >
> > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri
> > > >
> > > > mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
> > > >
> > > > threshold mask volume at 5
> > > >
> > > > mri_mask: could not read source volume brain.mgz
> > > >
> > > > ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/brain
> > .mgz
> > > >
> > > >
> > > > No such file or directory
> > > >
> > > > #--------------------------------------------
> > > >
> > > > #@# WM Segmentation Mon Feb 18 19:22:11 GMT 2013
> > > >
> > > > mri_segment brain.mgz wm.seg.mgz
> > > >
> > > > mri_segment: could not read source volume from brain.mgz
> > > >
> > > > ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/brain
> > .mgz
> > > >
> > > >
> > > > No such file or directory
> > > >
> > > > mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.mgz
> > wm.asegedit.mgz
> > > >
> > > > preserving editing changes in input volume...
> > > >
> > > > mri_edit_wm_with_aseg: could not read wm volume from wm.seg.mgz
> > > >
> > > > reading wm segmentation from wm.seg.mgz...
> > > >
> > > > ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.se
> > g.mg
> > > > z
> > > >
> > > > No such file or directory
> > > >
> > > > mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz
> > > >
> > > > mri_pretess: could not open wm.asegedit.mgz
> > > >
> > > > ERROR: cannotfind/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.as
> > eged
> > > > it.mgz
> > > >
> > > > No such file or directory
> > > >
> > > > #--------------------------------------------
> > > >
> > > > #@# Fill Mon Feb 18 19:22:11 GMT 2013
> > > >
> > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri
> > > >
> > > > mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta
> > > > -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz
> > > >
> > > > logging cutting plane coordinates to ../scripts/ponscc.cut.log...
> > > >
> > > > INFO: Using transforms/talairach.lta and its offset for Talairach volume
> > ...
> > > >
> > > > using segmentation aseg.auto_noCCseg.mgz...
> > > >
> > > > reading input volume...mri_fill: could not read wm.mgz
> > > >
> > > > ERROR: cannot find
> > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/mri/wm.mgz
> > > >
> > > > No such file or directory
> > > >
> > > > #--------------------------------------------
> > > >
> > > > #@# Tessellate lh Mon Feb 18 19:22:11 GMT 2013
> > > >
> > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
> > > >
> > > > mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz
> > > > ../mri/filled-pretess255.mgz
> > > >
> > > > mri_pretess: could not open ../mri/filled.mgz
> > > >
> > > > ERROR: cannot find ../mri/filled.mgz
> > > >
> > > > No such file or directory
> > > >
> > > > mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
> > > >
> > > > could not open ../mri/filled-pretess255.mgz
> > > >
> > > > ERROR: cannot find ../mri/filled-pretess255.mgz
> > > >
> > > > No such file or directory
> > > >
> > > > rm -f ../mri/filled-pretess255.mgz
> > > >
> > > > ?
> > > >
> > > > mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
> > > >
> > > > MRISread(../surf/lh.orig.nofix): could not open file
> > > >
> > > > No such file or directory
> > > >
> > > > Segmentation fault
> > > >
> > > > #--------------------------------------------
> > > >
> > > > #@# Smooth1 lh Mon Feb 18 19:22:12 GMT 2013
> > > >
> > > > mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix
> > ../surf/lh.smoothwm.nofix
> > > >
> > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
> > > >
> > > > setting seed for random number generator to 1234
> > > >
> > > > MRISread(../surf/lh.orig.nofix): could not open file
> > > >
> > > > No such file or directory
> > > >
> > > > mris_smooth: could not read surface file ../surf/lh.orig.nofix
> > > >
> > > > No such file or directory
> > > >
> > > > #--------------------------------------------
> > > >
> > > > #@# Inflation1 lh Mon Feb 18 19:22:12 GMT 2013
> > > >
> > > > mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix
> > > > ../surf/lh.inflated.nofix
> > > >
> > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
> > > >
> > > > MRISread(../surf/lh.smoothwm.nofix): could not open file
> > > >
> > > > Not saving sulc
> > > >
> > > > No such file or directory
> > > >
> > > > mris_inflate: could not read surface file ../surf/lh.smoothwm.nofix
> > > >
> > > > No such file or directory
> > > >
> > > > #--------------------------------------------
> > > >
> > > > #@# QSphere lh Mon Feb 18 19:22:12 GMT 2013
> > > >
> > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
> > > >
> > > > mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix
> > ../surf/lh.qsphere.nofix
> > > >
> > > > doing quick spherical unfolding.
> > > >
> > > > setting seed for random number genererator to 1234
> > > >
> > > > $Id: mris_sphere.c,v 1.47 2007/03/08 18:36:08 greve Exp $
> > > >
> > > > $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $
> > > >
> > > > MRISread(../surf/lh.inflated.nofix): could not open file
> > > >
> > > > No such file or directory
> > > >
> > > > mris_sphere: could not read surface file ../surf/lh.inflated.nofix
> > > >
> > > > No such file or directory
> > > >
> > > > #--------------------------------------------
> > > >
> > > > #@# Fix Topology lh Mon Feb 18 19:22:12 GMT 2013
> > > >
> > > > cp ../surf/lh.orig.nofix ../surf/lh.orig
> > > >
> > > > cp: cannot stat `../surf/lh.orig.nofix': No such file or directory
> > > >
> > > > cp ../surf/lh.inflated.nofix ../surf/lh.inflated
> > > >
> > > > cp: cannot stat `../surf/lh.inflated.nofix': No such file or directory
> > > >
> > > > /home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/scripts
> > > >
> > > > mris_fix_topology -mgz -sphere qsphere.nofix -ga -seed 1234
> > PREDEP40C_fsf lh
> > > >
> > > > reading spherical homeomorphism from 'qsphere.nofix'
> > > >
> > > > using genetic algorithm with optimized parameters
> > > >
> > > > setting seed for random number genererator to 1234
> > > >
> > > > *************************************************************
> > > >
> > > > Topology Correction Parameters
> > > >
> > > > retessellation mode: genetic search
> > > >
> > > > number of patches/generation : 10
> > > >
> > > > number of generations : 10
> > > >
> > > > surface mri loglikelihood coefficient : 1.0
> > > >
> > > > volume mri loglikelihood coefficient : 10.0
> > > >
> > > > normal dot loglikelihood coefficient : 1.0
> > > >
> > > > quadratic curvature loglikelihood coefficient : 1.0
> > > >
> > > > volume resolution : 2
> > > >
> > > > eliminate vertices during search : 1
> > > >
> > > > initial patch selection : 1
> > > >
> > > > select all defect vertices : 0
> > > >
> > > > ordering dependant retessellation: 0
> > > >
> > > > use precomputed edge table : 0
> > > >
> > > > smooth retessellated patch : 2
> > > >
> > > > match retessellated patch : 1
> > > >
> > > > verbose mode : 0
> > > >
> > > > *************************************************************
> > > >
> > > > INFO: assuming .mgz format
> > > >
> > > > $Id: mris_fix_topology.c,v 1.43 2007/01/05 16:57:16 nicks Exp $
> > > >
> > > > $Id: mrisurf.c,v 1.557.2.19 2009/08/05 22:10:21 nicks Exp $
> > > >
> > > >MRISread(/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf
> >
> > > > /lh.qsphere.nofix): could not open file
> > > >
> > > > reading inputsurface/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf/l
> > h.qsphe
> > > > re.nofix...
> > > >
> > > > No such file or directory
> > > >
> > > > mris_fix_topology: could not read inputsurface/home/k0933235/paul/PREDEP_Structural/subjects3/PREDEP40C_fsf/surf/l
> > h.qsphe
> > > > re.nofix
> > > >
> > > > No such file or directory
> > > >
> > > > mris_euler_number ../surf/lh.orig
> > > >
> > > > Linux ioplnx5.iop.kcl.ac.uk 2.6.32-279.19.1.el6.x86_64 #1 SMP Tue Dec 18
> > > > 17:22:54 CST 2012 x86_64 x86_64 x86_64 GNU/Linux
> > > >
> > > > recon-all exited with ERRORS at Mon Feb 18 19:22:12 GMT 2013
> > > >
> > > >  
> > > > > Date: Tue, 19 Feb 2013 16:35:50 -0500
> > > > > From: fischl@nmr.mgh.harvard.edu
> > > > > To: horton_paul@hotmail.com
> > > > > CC: freesurfer@nmr.mgh.harvard.edu
> > > > > Subject: Re: [Freesurfer] mri_ca_label problem
> > > > >
> > > > > Hi Paul
> > > > >
> > > > > is this within recon-all? Does that file exist? Can you check its
> > > > > permissions to make sure it is writeable? And that you have enough
> > disk
> > > > > space? Are any error messages printed?
> > > > > Bruce
> > > > >
> > > > >
> > > > > On Tue, 19 Feb 2013, paul horton wrote:
> > > > >
> > > > > > Hi guys,
> > > > > > I am wondering if you can help me.
> > > > > > I have run command: mri_ca_label -align -nobigventricles norm.mgz
> > > > > > transforms/talairach.m3z
> > $FREESURFER_HOME/average/RB_all_2008-03-26.gca
> > > > > > aseg.auto_noCCseg.mgz, on a 3T MPRAGE subject but it fails:  i.e. it
> > > > stops
> > > > > > after the 'saving intensity scales to
> > > > > > aseg.auto_noCCseg.label_intensities.txt' line and does not save the
> > > > file:
> > > > > > aseg.auto_noCCseg.mgz.  However, it does save the file:
> > > > > > aseg.auto_noCCseg.label_intensities.txt.  I have tried
> > > > > > it several times and it stops at the same place.  I have also tried
> > > > > > recon-all, where it jumps from
> > > > > > 'saving intensity scales to aseg.auto_noCCseg.label_intensities.txt'
> > to
> > > > the
> > > > > > command 'mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz',
> > where,
> > > > again,
> > > > > > the file: aseg.auto_noCCseg.mgz is not saved.  I am using freesurfer
> > > > version
> > > > > > 4.5.0.
> > > > > >  
> > > > > > So is there a way I can solve this problem.
> > > > > >  
> > > > > > Many Thanks
> > > > > > Paul
> > > > > > Ps, i have attached the output log below
> > > > > > ################
> > > > > > renormalizing sequences with structure alignment, equivalent to:
> > > > > >  -renormalize
> > > > > >  -renormalize_mean 0.500
> > > > > >  -regularize 0.500
> > > > > > not handling expanded ventricles...
> > > > > > reading 1 input volumes...
> > > > > > reading classifierarrayfrom/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-
> > 03-26
> > > > .gca
> > > > > > ...
> > > > > > reading input volume from norm.mgz...
> > > > > > average std[0] = 6.9
> > > > > > reading transform from transforms/talairach.m3z...
> > > > > > zcat transforms/talairach.m3z
> > > > > > Atlas used for the 3Dmorphwas/software/system/freesurfer/freesurfer-4.5.0//average/RB_all_2008-0
> > 3-26.
> > > > gca
> > > > > >
> > > > > > average std = 6.9   using min determinant for regularization = 4.7
> > > > > > 0 singular and 0 ill-conditioned covariance matrices regularized
> > > > > > labeling volume...
> > > > > > renormalizing by structure alignment....
> > > > > > renormalizing input #0
> > > > > > gca peak = 0.15151 (27)
> > > > > > mri peak = 0.15062 (23)
> > > > > > Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels,
> > > > > > overlap=0.484)
> > > > > > Left_Lateral_Ventricle (4): linear fit = 0.82 x + 0.0 (8178 voxels,
> > peak
> > > > =
> > > > > > 22), gca=22.3
> > > > > > gca peak = 0.14982 (20)
> > > > > > mri peak = 0.16025 (24)
> > > > > > Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984
> > voxels,
> > > > > > overlap=0.766)
> > > > > > Right_Lateral_Ventricle (43): linear fit = 1.02 x + 0.0 (6984
> > voxels,
> > > > peak =
> > > > > > 20), gca=20.5
> > > > > > gca peak = 0.28003 (97)
> > > > > > mri peak = 0.11295 (106)
> > > > > > Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels,
> > > > overlap=0.353)
> > > > > > Right_Pallidum (52): linear fit = 1.08 x + 0.0 (602 voxels, peak =
> > 104),
> > > > > > gca=104.3
> > > > > > gca peak = 0.18160 (96)
> > > > > > mri peak = 0.12433 (104)
> > > > > > Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels,
> > > > overlap=0.638)
> > > > > > Left_Pallidum (13): linear fit = 1.05 x + 0.0 (600 voxels, peak =
> > 101),
> > > > > > gca=100.8
> > > > > > gca peak = 0.27536 (62)
> > > > > > mri peak = 0.08252 (69)
> > > > > > Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels,
> > > > > > overlap=0.818)
> > > > > > Right_Hippocampus (53): linear fit = 1.10 x + 0.0 (1309 voxels, peak
> > =
> > > > 68),
> > > > > > gca=68.2
> > > > > > gca peak = 0.32745 (63)
> > > > > > mri peak = 0.07934 (66)
> > > > > > Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels,
> > > > > > overlap=1.000)
> > > > > > Left_Hippocampus (17): linear fit = 1.02 x + 0.0 (1133 voxels, peak
> > =
> > > > 65),
> > > > > > gca=64.6
> > > > > > gca peak = 0.08597 (105)
> > > > > > mri peak = 0.06861 (109)
> > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979
> > > > voxels,
> > > > > > overlap=0.744)
> > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.02 x + 0.0 (53979
> > > > voxels,
> > > > > > peak = 108), gca=107.6
> > > > > > gca peak = 0.09209 (106)
> > > > > > mri peak = 0.07113 (103)
> > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231
> > voxels,
> > > > > > overlap=0.820)
> > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231
> > voxels,
> > > > > > peak = 106), gca=106.0
> > > > > > gca peak = 0.07826 (63)
> > > > > > mri peak = 0.02785 (72)
> > > > > > Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels,
> > > > > > overlap=0.547)
> > > > > > Left_Cerebral_Cortex (3): linear fit = 1.12 x + 0.0 (79920 voxels,
> > peak
> > > > =
> > > > > > 71), gca=70.9
> > > > > > gca peak = 0.08598 (64)
> > > > > > mri peak = 0.02894 (68)
> > > > > > Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels,
> > > > > > overlap=0.642)
> > > > > > Right_Cerebral_Cortex (42): linear fit = 1.08 x + 0.0 (80258 voxels,
> > > > peak =
> > > > > > 69), gca=68.8
> > > > > > gca peak = 0.24164 (71)
> > > > > > mri peak = 0.13663 (85)
> > > > > > Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels,
> > > > overlap=0.000)
> > > > > > Right_Caudate (50): linear fit = 1.15 x + 0.0 (1108 voxels, peak =
> > 82),
> > > > > > gca=81.7
> > > > > > gca peak = 0.18227 (75)
> > > > > > mri peak = 0.14739 (80)
> > > > > > Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels,
> > > > overlap=0.988)
> > > > > > Left_Caudate (11): linear fit = 1.02 x + 0.0 (1205 voxels, peak =
> > 77),
> > > > > > gca=76.9
> > > > > > gca peak = 0.10629 (62)
> > > > > > mri peak = 0.05203 (64)
> > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
> > > > > > overlap=0.948)
> > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
> > > > peak =
> > > > > > 64), gca=63.5
> > > > > > gca peak = 0.11668 (59)
> > > > > > mri peak = 0.05041 (65)
> > > > > > Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689
> > voxels,
> > > > > > overlap=0.926)
> > > > > > Right_Cerebellum_Cortex (47): linear fit = 1.08 x + 0.0 (39689
> > voxels,
> > > > peak
> > > > > > = 63), gca=63.4
> > > > > > gca peak = 0.17849 (88)
> > > > > > mri peak = 0.09573 (95)
> > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309
> > > > voxels,
> > > > > > overlap=0.601)
> > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.08 x + 0.0 (5309
> > > > voxels,
> > > > > > peak = 95), gca=94.6
> > > > > > gca peak = 0.16819 (86)
> > > > > > mri peak = 0.10076 (95)
> > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881
> > > > voxels,
> > > > > > overlap=0.590)
> > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.08 x + 0.0 (5881
> > > > voxels,
> > > > > > peak = 92), gca=92.5
> > > > > > gca peak = 0.41688 (64)
> > > > > > mri peak = 0.07820 (67)
> > > > > > Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels,
> > > > overlap=1.000)
> > > > > > Left_Amygdala (18): linear fit = 1.02 x + 0.0 (597 voxels, peak =
> > 66),
> > > > > > gca=65.6
> > > > > > gca peak = 0.42394 (62)
> > > > > > mri peak = 0.10919 (71)
> > > > > > Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels,
> > > > overlap=0.434)
> > > > > > Right_Amygdala (54): linear fit = 1.12 x + 0.0 (570 voxels, peak =
> > 70),
> > > > > > gca=69.8
> > > > > > gca peak = 0.10041 (96)
> > > > > > mri peak = 0.07146 (97)
> > > > > > Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels,
> > > > > > overlap=0.910)
> > > > > > Left_Thalamus_Proper (10): linear fit = 1.02 x + 0.0 (4505 voxels,
> > peak
> > > > =
> > > > > > 98), gca=98.4
> > > > > > gca peak = 0.13978 (88)
> > > > > > mri peak = 0.06159 (103)
> > > > > > Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels,
> > > > > > overlap=0.376)
> > > > > > Right_Thalamus_Proper (49): linear fit = 1.12 x + 0.0 (4569 voxels,
> > peak
> > > > =
> > > > > > 99), gca=99.0
> > > > > > gca peak = 0.08514 (81)
> > > > > > mri peak = 0.06222 (85)
> > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels,
> > > > overlap=0.964)
> > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak =
> > 81),
> > > > > > gca=81.0
> > > > > > gca peak = 0.09624 (82)
> > > > > > mri peak = 0.09383 (84)
> > > > > > Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels,
> > > > overlap=0.815)
> > > > > > Right_Putamen (51): linear fit = 1.02 x + 0.0 (2273 voxels, peak =
> > 84),
> > > > > > gca=84.0
> > > > > > gca peak = 0.07543 (88)
> > > > > > mri peak = 0.05306 (86)
> > > > > > Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels,
> > overlap=0.765)
> > > > > > Brain_Stem (16): linear fit = 1.05 x + 0.0 (12748 voxels, peak =
> > 92),
> > > > > > gca=92.4
> > > > > > gca peak = 0.12757 (95)
> > > > > > mri peak = 0.05862 (107)
> > > > > > Right_VentralDC: unreasonable value (111.6/107.0), not in range [80,
> > > > 110] -
> > > > > > rejecting
> > > > > > gca peak = 0.17004 (92)
> > > > > > mri peak = 0.06574 (111)
> > > > > > Left_VentralDC: unreasonable value (105.8/111.0), not in range [80,
> > 110]
> > > > -
> > > > > > rejecting
> > > > > > gca peak = 0.21361 (36)
> > > > > > mri peak = 0.12619 (24)
> > > > > > Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels,
> > > > overlap=0.000)
> > > > > > Third_Ventricle (14): linear fit = 0.70 x + 0.0 (208 voxels, peak =
> > 25),
> > > > > > gca=25.2
> > > > > > gca peak = 0.26069 (23)
> > > > > > mri peak = 0.16285 (24)
> > > > > > Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels,
> > > > overlap=0.640)
> > > > > > Fourth_Ventricle (15): linear fit = 0.90 x + 0.0 (667 voxels, peak =
> > > > 21),
> > > > > > gca=20.7
> > > > > > gca peak Unknown = 0.94427 ( 0)
> > > > > > gca peak Left_Inf_Lat_Vent = 0.31795 (35)
> > > > > > gca peak CSF = 0.14367 (38)
> > > > > > gca peak Left_Accumbens_area = 0.57033 (70)
> > > > > > gca peak Left_VentralDC = 0.17004 (92)
> > > > > > gca peak Left_undetermined = 1.00000 (35)
> > > > > > gca peak Left_vessel = 0.65201 (62)
> > > > > > gca peak Left_choroid_plexus = 0.09084 (48)
> > > > > > gca peak Right_Inf_Lat_Vent = 0.31129 (32)
> > > > > > gca peak Right_Accumbens_area = 0.30219 (72)
> > > > > > gca peak Right_VentralDC = 0.12757 (95)
> > > > > > gca peak Right_vessel = 0.83418 (60)
> > > > > > gca peak Right_choroid_plexus = 0.10189 (48)
> > > > > > gca peak Fifth_Ventricle = 0.72939 (42)
> > > > > > gca peak WM_hypointensities = 0.14821 (82)
> > > > > > gca peak non_WM_hypointensities = 0.10354 (53)
> > > > > > gca peak Optic_Chiasm = 0.34849 (76)
> > > > > > not using caudate to estimate GM means
> > > > > > estimating mean gm scale to be 1.08 x + 0.0
> > > > > > estimating mean wm scale to be 1.01 x + 0.0
> > > > > > estimating mean csf scale to be 0.86 x + 0.0
> > > > > > Left_Pallidum too bright - rescaling by 1.007 (from 1.050) to 101.5
> > (was
> > > > > > 100.8)
> > > > > > Right_Pallidum too bright - rescaling by 0.973 (from 1.075) to 101.5
> > > > (was
> > > > > > 104.3)
> > > > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
> > > > > > renormalizing by structure alignment....
> > > > > > renormalizing input #0
> > > > > > gca peak = 0.14515 (23)
> > > > > > mri peak = 0.15062 (23)
> > > > > > Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels,
> > > > > > overlap=0.897)
> > > > > > Left_Lateral_Ventricle (4): linear fit = 1.02 x + 0.0 (8178 voxels,
> > peak
> > > > =
> > > > > > 24), gca=23.6
> > > > > > gca peak = 0.19392 (21)
> > > > > > mri peak = 0.16025 (24)
> > > > > > Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984
> > voxels,
> > > > > > overlap=0.745)
> > > > > > Right_Lateral_Ventricle (43): linear fit = 1.00 x + 0.0 (6984
> > voxels,
> > > > peak =
> > > > > > 21), gca=21.0
> > > > > > gca peak = 0.25607 (102)
> > > > > > mri peak = 0.11295 (106)
> > > > > > Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels,
> > > > overlap=1.000)
> > > > > > Right_Pallidum (52): linear fit = 1.02 x + 0.0 (602 voxels, peak =
> > 105),
> > > > > > gca=104.5
> > > > > > gca peak = 0.17462 (103)
> > > > > > mri peak = 0.12433 (104)
> > > > > > Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels,
> > > > overlap=0.999)
> > > > > > Left_Pallidum (13): linear fit = 1.00 x + 0.0 (600 voxels, peak =
> > 103),
> > > > > > gca=103.0
> > > > > > gca peak = 0.24759 (68)
> > > > > > mri peak = 0.08252 (69)
> > > > > > Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels,
> > > > > > overlap=0.999)
> > > > > > Right_Hippocampus (53): linear fit = 1.00 x + 0.0 (1309 voxels, peak
> > =
> > > > 68),
> > > > > > gca=68.0
> > > > > > gca peak = 0.28061 (65)
> > > > > > mri peak = 0.07934 (66)
> > > > > > Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels,
> > > > > > overlap=0.999)
> > > > > > Left_Hippocampus (17): linear fit = 0.95 x + 0.0 (1133 voxels, peak
> > =
> > > > 62),
> > > > > > gca=61.8
> > > > > > gca peak = 0.08360 (108)
> > > > > > mri peak = 0.06861 (109)
> > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979
> > > > voxels,
> > > > > > overlap=0.831)
> > > > > > Right_Cerebral_White_Matter (41): linear fit = 1.00 x + 0.0 (53979
> > > > voxels,
> > > > > > peak = 108), gca=108.0
> > > > > > gca peak = 0.09206 (106)
> > > > > > mri peak = 0.07113 (103)
> > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231
> > voxels,
> > > > > > overlap=0.820)
> > > > > > Left_Cerebral_White_Matter (2): linear fit = 1.00 x + 0.0 (49231
> > voxels,
> > > > > > peak = 106), gca=106.0
> > > > > > gca peak = 0.06916 (71)
> > > > > > mri peak = 0.02785 (72)
> > > > > > Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels,
> > > > > > overlap=0.733)
> > > > > > Left_Cerebral_Cortex (3): linear fit = 0.98 x + 0.0 (79920 voxels,
> > peak
> > > > =
> > > > > > 69), gca=69.2
> > > > > > gca peak = 0.08227 (69)
> > > > > > mri peak = 0.02894 (68)
> > > > > > Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels,
> > > > > > overlap=0.734)
> > > > > > Right_Cerebral_Cortex (42): linear fit = 1.00 x + 0.0 (80258 voxels,
> > > > peak =
> > > > > > 69), gca=69.0
> > > > > > gca peak = 0.22329 (81)
> > > > > > mri peak = 0.13663 (85)
> > > > > > Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels,
> > > > overlap=1.000)
> > > > > > Right_Caudate (50): linear fit = 1.00 x + 0.0 (1108 voxels, peak =
> > 81),
> > > > > > gca=81.0
> > > > > > gca peak = 0.18180 (77)
> > > > > > mri peak = 0.14739 (80)
> > > > > > Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels,
> > > > overlap=0.937)
> > > > > > Left_Caudate (11): linear fit = 1.00 x + 0.0 (1205 voxels, peak =
> > 77),
> > > > > > gca=77.0
> > > > > > gca peak = 0.10419 (63)
> > > > > > mri peak = 0.05203 (64)
> > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
> > > > > > overlap=0.982)
> > > > > > Left_Cerebellum_Cortex (8): linear fit = 1.02 x + 0.0 (38823 voxels,
> > > > peak =
> > > > > > 65), gca=64.6
> > > > > > gca peak = 0.12084 (64)
> > > > > > mri peak = 0.05041 (65)
> > > > > > Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689
> > voxels,
> > > > > > overlap=0.985)
> > > > > > Right_Cerebellum_Cortex (47): linear fit = 0.98 x + 0.0 (39689
> > voxels,
> > > > peak
> > > > > > = 62), gca=62.4
> > > > > > gca peak = 0.17137 (94)
> > > > > > mri peak = 0.09573 (95)
> > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309
> > > > voxels,
> > > > > > overlap=0.978)
> > > > > > Left_Cerebellum_White_Matter (7): linear fit = 1.00 x + 0.0 (5309
> > > > voxels,
> > > > > > peak = 94), gca=94.0
> > > > > > gca peak = 0.15715 (93)
> > > > > > mri peak = 0.10076 (95)
> > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881
> > > > voxels,
> > > > > > overlap=0.983)
> > > > > > Right_Cerebellum_White_Matter (46): linear fit = 1.00 x + 0.0 (5881
> > > > voxels,
> > > > > > peak = 93), gca=93.0
> > > > > > gca peak = 0.32238 (65)
> > > > > > mri peak = 0.07820 (67)
> > > > > > Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels,
> > > > overlap=1.000)
> > > > > > Left_Amygdala (18): linear fit = 1.00 x + 0.0 (597 voxels, peak =
> > 65),
> > > > > > gca=65.0
> > > > > > gca peak = 0.49832 (70)
> > > > > > mri peak = 0.10919 (71)
> > > > > > Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels,
> > > > overlap=1.000)
> > > > > > Right_Amygdala (54): linear fit = 1.00 x + 0.0 (570 voxels, peak =
> > 70),
> > > > > > gca=70.0
> > > > > > gca peak = 0.10606 (98)
> > > > > > mri peak = 0.07146 (97)
> > > > > > Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels,
> > > > > > overlap=0.901)
> > > > > > Left_Thalamus_Proper (10): linear fit = 1.00 x + 0.0 (4505 voxels,
> > peak
> > > > =
> > > > > > 98), gca=98.0
> > > > > > gca peak = 0.12505 (99)
> > > > > > mri peak = 0.06159 (103)
> > > > > > Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels,
> > > > > > overlap=0.961)
> > > > > > Right_Thalamus_Proper (49): linear fit = 1.00 x + 0.0 (4569 voxels,
> > peak
> > > > =
> > > > > > 99), gca=99.0
> > > > > > gca peak = 0.08514 (81)
> > > > > > mri peak = 0.06222 (85)
> > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels,
> > > > overlap=0.964)
> > > > > > Left_Putamen (12): linear fit = 1.00 x + 0.0 (2799 voxels, peak =
> > 81),
> > > > > > gca=81.0
> > > > > > gca peak = 0.09838 (78)
> > > > > > mri peak = 0.09383 (84)
> > > > > > Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels,
> > > > overlap=0.982)
> > > > > > Right_Putamen (51): linear fit = 1.00 x + 0.0 (2273 voxels, peak =
> > 78),
> > > > > > gca=78.0
> > > > > > gca peak = 0.07177 (90)
> > > > > > mri peak = 0.05306 (86)
> > > > > > Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels,
> > overlap=0.860)
> > > > > > Brain_Stem (16): linear fit = 1.02 x + 0.0 (12748 voxels, peak =
> > 92),
> > > > > > gca=92.2
> > > > > > gca peak = 0.13316 (95)
> > > > > > mri peak = 0.05862 (107)
> > > > > > Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels,
> > > > overlap=0.010)
> > > > > > Right_VentralDC (60): linear fit = 1.15 x + 0.0 (1664 voxels, peak =
> > > > 109),
> > > > > > gca=109.2
> > > > > > gca peak = 0.16834 (92)
> > > > > > mri peak = 0.06574 (111)
> > > > > > Left_VentralDC: unreasonable value (105.8/111.0), not in range [80,
> > 110]
> > > > -
> > > > > > rejecting
> > > > > > gca peak = 0.25342 (25)
> > > > > > mri peak = 0.12619 (24)
> > > > > > Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels,
> > > > overlap=0.998)
> > > > > > Third_Ventricle (14): linear fit = 1.00 x + 0.0 (208 voxels, peak =
> > 25),
> > > > > > gca=25.0
> > > > > > gca peak = 0.20850 (21)
> > > > > > mri peak = 0.16285 (24)
> > > > > > Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels,
> > > > overlap=0.808)
> > > > > > Fourth_Ventricle (15): linear fit = 1.02 x + 0.0 (667 voxels, peak =
> > > > 22),
> > > > > > gca=21.5
> > > > > > gca peak Unknown = 0.94427 ( 0)
> > > > > > gca peak Left_Inf_Lat_Vent = 0.26363 (36)
> > > > > > gca peak CSF = 0.17919 (33)
> > > > > > gca peak Left_Accumbens_area = 0.40223 (72)
> > > > > > gca peak Left_VentralDC = 0.16834 (92)
> > > > > > gca peak Left_undetermined = 1.00000 (35)
> > > > > > gca peak Left_vessel = 0.63670 (62)
> > > > > > gca peak Left_choroid_plexus = 0.09084 (48)
> > > > > > gca peak Right_Inf_Lat_Vent = 0.29122 (35)
> > > > > > gca peak Right_Accumbens_area = 0.25605 (83)
> > > > > > gca peak Right_vessel = 0.83418 (60)
> > > > > > gca peak Right_choroid_plexus = 0.10189 (48)
> > > > > > gca peak Fifth_Ventricle = 0.81716 (36)
> > > > > > gca peak WM_hypointensities = 0.15216 (83)
> > > > > > gca peak non_WM_hypointensities = 0.09346 (54)
> > > > > > gca peak Optic_Chiasm = 0.34849 (76)
> > > > > > not using caudate to estimate GM means
> > > > > > setting label Right_VentralDC based on Left_VentralDC = 1.15 x +  0
> > > > > > estimating mean gm scale to be 0.99 x + 0.0
> > > > > > estimating mean wm scale to be 1.00 x + 0.0
> > > > > > estimating mean csf scale to be 1.01 x + 0.0
> > > > > > Left_Pallidum too bright - rescaling by 0.987 (from 1.000) to 101.6
> > (was
> > > > > > 103.0)
> > > > > > Right_Pallidum too bright - rescaling by 0.972 (from 1.025) to 101.6
> > > > (was
> > > > > > 104.5)
> > > > > > saving intensity scales to aseg.auto_noCCseg.label_intensities.txt
> > > > > >
> > > > > >  
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